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Fixed older GS reported bug. Actually, the problem really lies in Picard (can't set max records in RAM without it throwing an exception, reported on their JIRA) so I just masked out the problem by removing this never-used argument from this rarely-used tool.

This commit is contained in:
Eric Banks 2012-07-31 16:00:36 -04:00
parent ab53d73459
commit 6cb10cef96
2 changed files with 2 additions and 13 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/io/storage/SAMFileWriterStorage.java
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@ -62,6 +62,7 @@ public class SAMFileWriterStorage implements SAMFileWriter, Storage<SAMFileWrite
if (stub.getGenerateMD5())
factory.setCreateMd5File(true);
// Adjust max records in RAM.
// TODO -- this doesn't actually work because of a bug in Picard; do not use until fixed
if(stub.getMaxRecordsInRam() != null)
factory.setMaxRecordsInRam(stub.getMaxRecordsInRam());

14
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java
View File

@ -73,19 +73,7 @@ public class LeftAlignIndels extends ReadWalker<Integer, Integer> {
@Output(required=false, doc="Output bam")
protected StingSAMFileWriter writer = null;
/**
* If set too low, the tool may run out of system file descriptors needed to perform sorting; if too high, the tool
* may run out of memory. We recommend that you additionally tell Java to use a temp directory with plenty of available
* space (by setting java.io.tempdir on the command-line).
*/
@Argument(fullName="maxReadsInRam", shortName="maxInRam", doc="max reads allowed to be kept in memory at a time by the output writer", required=false)
protected int MAX_RECORDS_IN_RAM = 500000;
public void initialize() {
// set up the output writer
if ( writer != null )
writer.setMaxRecordsInRam(MAX_RECORDS_IN_RAM);
}
public void initialize() {}
private void emit(final SAMRecord read) {
if ( writer != null )